Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 66 of 216
Found at i:19804778 original size:23 final size:23
Alignment explanation
Indices: 19804752--19804814 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
19804742 TCTAAAATAT
19804752 CCAAATAATATTATAAACGACAA
1 CCAAATAATATTATAAACGACAA
*
19804775 CCAAATAATATTAAAAACGACAA
1 CCAAATAATATTATAAACGACAA
* * *
19804798 CGAAACAATATAATAAA
1 CCAAATAATATTATAAA
19804815 AAGCTGCGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (23 bp):
CCAAATAATATTATAAACGACAA
Found at i:19805003 original size:3 final size:3
Alignment explanation
Indices: 19804995--19805028 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
19804985 AACATCGTCC
19804995 TCA TCA TCA TCA TCA TCA TCA TCA TTC- TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA -TCA TCA TCA T
19805029 TCCTAAACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:19811673 original size:18 final size:18
Alignment explanation
Indices: 19811650--19811687 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
19811640 CAAGGGTTTC
*
19811650 TCAATTGGTACTTATCAA
1 TCAATTGGAACTTATCAA
19811668 TCAATTGGAACTTATCAA
1 TCAATTGGAACTTATCAA
19811686 TC
1 TC
19811688 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (18 bp):
TCAATTGGAACTTATCAA
Found at i:19812219 original size:17 final size:17
Alignment explanation
Indices: 19812182--19812226 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
19812172 CTCTTAAAAG
* *
19812182 AGTTCATCAAACCCTAG
1 AGTTCACCAAACCCTAA
*
19812199 AGTTCACCAAACCTTAA
1 AGTTCACCAAACCCTAA
*
19812216 AGTTCGCCAAA
1 AGTTCACCAAA
19812227 TGAAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (17 bp):
AGTTCACCAAACCCTAA
Found at i:19816405 original size:22 final size:23
Alignment explanation
Indices: 19816380--19816430 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
19816370 CACGTATATT
*
19816380 TTAAAAT-ATATCAAACATTT-CA
1 TTAAAATGA-ATCAAACATTTGAA
*
19816402 TTAAAATGAGTCAAACATTTGAA
1 TTAAAATGAATCAAACATTTGAA
19816425 TTAAAA
1 TTAAAA
19816431 CCATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (23 bp):
TTAAAATGAATCAAACATTTGAA
Found at i:19816437 original size:22 final size:21
Alignment explanation
Indices: 19816389--19816438 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
19816379 TTTAAAATAT
* **
19816389 ATCAAACATTTCATTAAAATG
1 ATCAAACATTTAATTAAAACC
19816410 AGTCAAACATTTGAATTAAAACC
1 A-TCAAACATTT-AATTAAAACC
19816433 ATCAAA
1 ATCAAA
19816439 ATTGATGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (21 bp):
ATCAAACATTTAATTAAAACC
Found at i:19818080 original size:50 final size:50
Alignment explanation
Indices: 19817962--19818242 Score: 248
Period size: 50 Copynumber: 5.5 Consensus size: 50
19817952 ATGCCAAATC
* * *
19817962 CATGTCCCAGACATGGTCTTACATGGAATG-TTTCATGTAC--TGCCAATGT
1 CATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATAT-CGGTGCCAATGT
* * * * * *
19818011 TATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCCCATGT
1 CATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGT
* * *
19818061 CATGTCCCAGACATGGTCTTAC--GGGAGACCTCTTATCTCGGTGCCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGAG--CTCTCATATCGGTGCCAATGT
* * * * *
19818111 CATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGATGCCAACGT
1 CATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGT
* * * *
19818161 CATGTCCCAGACATGGTTTTACATGGGACCTCTCATGATCTCAAGGATACCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT-A--TC--GG-TGCCAATGT
19818217 CATGTCCCAGACATGGTCTTACATGG
1 CATGTCCCAGACATGGTCTTACATGG
19818243 AATCTCTTTA
Statistics
Matches: 188, Mismatches: 31, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
48 7 0.04
49 29 0.15
50 114 0.61
52 4 0.02
53 2 0.01
55 1 0.01
56 31 0.16
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGT
Found at i:19818132 original size:100 final size:104
Alignment explanation
Indices: 19818015--19818242 Score: 286
Period size: 100 Copynumber: 2.2 Consensus size: 104
19818005 CAATGTTATA
* * ** * * *
19818015 TCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCCCATGTCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAACGTCATGTCCCAGACATGGTCT
*
19818080 TAC-GGGAGACCTCT-T-ATCTC-GG-TGCCAATGCCATG
66 TACAGGG-GACCTCTATGATCTCAGGATACCAATGCCATG
* * *
19818115 TCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGATGCCAACGTCATGTCCCAGACATGGTTT
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAACGTCATGTCCCAGACATGGTCT
*
19818180 TACATGGGACCTCTCATGATCTCAAGGATACCAATGCCATG
66 TACAGGGGACCTCT-ATGATCTC-AGGATACCAATGCCATG
19818221 TCCCAGACATGGTCTTACATGG
1 TCCCAGACATGGTCTTACATGG
19818243 AATCTCTTTA
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
100 65 0.60
101 2 0.02
102 1 0.01
103 5 0.05
105 2 0.02
106 34 0.31
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (104 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAACGTCATGTCCCAGACATGGTCT
TACAGGGGACCTCTATGATCTCAGGATACCAATGCCATG
Found at i:19820831 original size:28 final size:28
Alignment explanation
Indices: 19820800--19820903 Score: 88
Period size: 28 Copynumber: 3.8 Consensus size: 28
19820790 TAAAAAATAA
*
19820800 AATAAACATACATTACCAAAACTATCTT
1 AATAAACATACACTACCAAAACTATCTT
* ** ** ** *
19820828 AATACACA-ATTCTAATAATTCTA-CTAA
1 AATAAACATACACTACCAAAACTATCT-T
*
19820855 AATAAACATGCACTACCAAAACTATCTT
1 AATAAACATACACTACCAAAACTATCTT
19820883 AATAAACATACACTA-CAAAAC
1 AATAAACATACACTACCAAAAC
19820904 AAACATACAT
Statistics
Matches: 54, Mismatches: 19, Indels: 7
0.68 0.24 0.09
Matches are distributed among these distances:
26 2 0.04
27 21 0.39
28 29 0.54
29 2 0.04
ACGTcount: A:0.51, C:0.22, G:0.01, T:0.26
Consensus pattern (28 bp):
AATAAACATACACTACCAAAACTATCTT
Found at i:19820915 original size:28 final size:28
Alignment explanation
Indices: 19820855--19820915 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
19820845 ATTCTACTAA
* * * *
19820855 AATAAACATGCACTACCAAAACTATCTT
1 AATAAACATACACTACCAAAACAAACAT
19820883 AATAAACATACACTA-CAAAACAAACAT
1 AATAAACATACACTACCAAAACAAACAT
19820910 ACATAA
1 A-ATAA
19820916 TTCTAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.56, C:0.23, G:0.02, T:0.20
Consensus pattern (28 bp):
AATAAACATACACTACCAAAACAAACAT
Found at i:19821042 original size:19 final size:19
Alignment explanation
Indices: 19821015--19821051 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19821005 AAAAAGAAAA
19821015 TTTTAACACAAATCTAAAT
1 TTTTAACACAAATCTAAAT
*
19821034 TTTTGACACAAATCTAAA
1 TTTTAACACAAATCTAAA
19821052 CTAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (19 bp):
TTTTAACACAAATCTAAAT
Found at i:19822625 original size:19 final size:19
Alignment explanation
Indices: 19822601--19822637 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19822591 TCATTTAAAA
19822601 ATTTTAAAAAATAAAAATC
1 ATTTTAAAAAATAAAAATC
* *
19822620 ATTTTAGAAAATTAAAAT
1 ATTTTAAAAAATAAAAAT
19822638 TATTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
ATTTTAAAAAATAAAAATC
Found at i:19827033 original size:29 final size:30
Alignment explanation
Indices: 19826968--19827033 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
19826958 TACAAACTCC
*
19826968 ACTTGATTGCATTAATATAAGTAAATTATT
1 ACTTGATTGCATTAATATAAATAAATTATT
** *
19826998 TGTTGATTGTATTAATATAAAT-AATTATT
1 ACTTGATTGCATTAATATAAATAAATTATT
19827027 ACTTGAT
1 ACTTGAT
19827034 AGACGTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (30 bp):
ACTTGATTGCATTAATATAAATAAATTATT
Found at i:19828004 original size:18 final size:19
Alignment explanation
Indices: 19827983--19828029 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
19827973 GTCATTTATA
19827983 AAAATATTTTAATT-CAAT
1 AAAATATTTTAATTACAAT
19828001 AAAA-ATATTTAATTACAAT
1 AAAATAT-TTTAATTACAAT
*
19828020 GAAAT-TTTTA
1 AAAATATTTTA
19828030 TTATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 15 0.60
19 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATATTTTAATTACAAT
Found at i:19828004 original size:19 final size:19
Alignment explanation
Indices: 19827980--19828019 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
19827970 AAAGTCATTT
19827980 ATAAAAATATTTTAATT-CA
1 ATAAAAATA-TTTAATTACA
19827999 ATAAAAATATTTAATTACA
1 ATAAAAATATTTAATTACA
19828018 AT
1 AT
19828020 GAAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAATATTTAATTACA
Found at i:19833075 original size:16 final size:16
Alignment explanation
Indices: 19833054--19833092 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
19833044 AAAAGCTACT
19833054 CACCACGTTGGCACAA
1 CACCACGTTGGCACAA
19833070 CACCACGTTGGCACAA
1 CACCACGTTGGCACAA
19833086 CTACCAC
1 C-ACCAC
19833093 TACCAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.31, C:0.41, G:0.15, T:0.13
Consensus pattern (16 bp):
CACCACGTTGGCACAA
Found at i:19836419 original size:9 final size:9
Alignment explanation
Indices: 19836407--19836540 Score: 62
Period size: 9 Copynumber: 14.7 Consensus size: 9
19836397 AAATTAAAAA
*
19836407 AAAAACTTT
1 AAAAATTTT
19836416 AAAAATATTT
1 AAAAAT-TTT
* **
19836426 TAAAATTAA
1 AAAAATTTT
19836435 AAAAATTTT
1 AAAAATTTT
19836444 AAAAATTTT
1 AAAAATTTT
19836453 AAAAAGTATTT
1 AAAAA-T-TTT
19836464 GAAAAATATTT
1 -AAAAAT-TTT
* *
19836475 TAAAA-TTA
1 AAAAATTTT
**
19836483 AAAAATAAT
1 AAAAATTTT
19836492 AAAAA---T
1 AAAAATTTT
*
19836498 AAAGTATTTT
1 AAA-AATTTT
19836508 AAAAATATTT
1 AAAAAT-TTT
* *
19836518 TAAAA-TTA
1 AAAAATTTT
*
19836526 AAAAAATTT
1 AAAAATTTT
19836535 AAAAAT
1 AAAAAT
19836541 AAATATATTT
Statistics
Matches: 94, Mismatches: 20, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
6 4 0.04
7 1 0.01
8 12 0.13
9 40 0.43
10 24 0.26
11 8 0.09
12 5 0.05
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAAATTTT
Found at i:19836436 original size:17 final size:17
Alignment explanation
Indices: 19836414--19836447 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19836404 AAAAAAAACT
*
19836414 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTTAAAA
19836431 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
19836448 ATTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:19836445 original size:28 final size:27
Alignment explanation
Indices: 19836390--19836457 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
19836380 TCAAAAATTT
19836390 ATTTTAAAAATTAAAAAAAAAACTTTAAAA
1 ATTTTAAAAATT---AAAAAAACTTTAAAA
* *
19836420 ATATTTTAAAATTAAAAAAATTTTAAAA
1 AT-TTTAAAAATTAAAAAAACTTTAAAA
19836448 ATTTTAAAAA
1 ATTTTAAAAA
19836458 GTATTTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 7 0.21
28 16 0.47
30 2 0.06
31 9 0.26
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTTTAAAAATTAAAAAAACTTTAAAA
Found at i:19836449 original size:49 final size:47
Alignment explanation
Indices: 19836392--19836540 Score: 173
Period size: 49 Copynumber: 3.2 Consensus size: 47
19836382 AAAAATTTAT
**
19836392 TTTAAAAATTAAAAAAAAAACTTTAAAAATATTTTAAAATTAAAAAAA
1 TTTAAAAATTAAAAAAAGTA-TTTAAAAATATTTTAAAATTAAAAAAA
**
19836440 TTTTAAAAATTTTAAAAAGTATTTGAAAAATATTTTAAAATT-AAAAAA
1 -TTTAAAAATTAAAAAAAGTATTT-AAAAATATTTTAAAATTAAAAAAA
* *
19836488 --TAATAA--AAATAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA
1 TTTAAAAATTAAAAAAAGTA-TTTAAAAATATTTTAAAATTAAAAAAA
19836532 TTTAAAAAT
1 TTTAAAAAT
19836541 AAATATATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
43 24 0.28
44 9 0.11
45 5 0.06
46 5 0.06
48 9 0.11
49 33 0.39
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.36
Consensus pattern (47 bp):
TTTAAAAATTAAAAAAAGTATTTAAAAATATTTTAAAATTAAAAAAA
Found at i:19836463 original size:12 final size:11
Alignment explanation
Indices: 19836413--19836479 Score: 58
Period size: 11 Copynumber: 6.6 Consensus size: 11
19836403 AAAAAAAAAC
19836413 TTTAAAAATAT
1 TTTAAAAATAT
19836424 TTT--AAA-A-
1 TTTAAAAATAT
*
19836431 -TTAAAAAAAT
1 TTTAAAAATAT
19836441 TTT-AAAA-AT
1 TTTAAAAATAT
19836450 TTTAAAAAGTAT
1 TTTAAAAA-TAT
*
19836462 TTGAAAAATAT
1 TTTAAAAATAT
19836473 TTTAAAA
1 TTTAAAA
19836480 TTAAAAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
6 2 0.04
8 4 0.09
9 9 0.20
10 8 0.17
11 14 0.30
12 9 0.20
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
TTTAAAAATAT
Found at i:19836502 original size:43 final size:43
Alignment explanation
Indices: 19836455--19836543 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
19836445 AAAATTTTAA
*
19836455 AAAGTATTTGAAAAATATTTTAAAATTAAAAAATAATAAAAAT
1 AAAGTATTTGAAAAATATTTTAAAATTAAAAAATATTAAAAAT
*
19836498 AAAGTATTTTAAAAATATTTTAAAATTAAAAAA-ATTTAAAAAT
1 AAAGTATTTGAAAAATATTTTAAAATTAAAAAATA-TTAAAAAT
19836541 AAA
1 AAA
19836544 TATATTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (43 bp):
AAAGTATTTGAAAAATATTTTAAAATTAAAAAATATTAAAAAT
Found at i:19836526 original size:17 final size:17
Alignment explanation
Indices: 19836506--19836550 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
19836496 ATAAAGTATT
19836506 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
19836523 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
19836539 ATAAATATATTT
1 TTAAAAATATTT
19836551 ATTATATCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:19836528 original size:16 final size:16
Alignment explanation
Indices: 19836466--19836550 Score: 54
Period size: 16 Copynumber: 5.6 Consensus size: 16
19836456 AAGTATTTGA
*
19836466 AAAATATTTTAAAATT
1 AAAATATTTTAAAAAT
* **
19836482 AAAAAATAATAAAAAT
1 AAAATATTTTAAAAAT
*
19836498 AAAGTATTTT----A-
1 AAAATATTTTAAAAAT
*
19836509 AAAATATTTTAAAATT
1 AAAATATTTTAAAAAT
* *
19836525 AAAAAAATTTAAAAAT
1 AAAATATTTTAAAAAT
19836541 AAATATATTT
1 AAA-ATATTT
19836551 ATTATATCGG
Statistics
Matches: 48, Mismatches: 15, Indels: 11
0.65 0.20 0.15
Matches are distributed among these distances:
11 9 0.19
12 1 0.02
16 34 0.71
17 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (16 bp):
AAAATATTTTAAAAAT
Found at i:19838981 original size:7 final size:7
Alignment explanation
Indices: 19838969--19839004 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
19838959 GACTGTCGGT
19838969 CCTTTTA
1 CCTTTTA
19838976 CCTTTTA
1 CCTTTTA
19838983 CCTTTTA
1 CCTTTTA
19838990 CCTTTTA
1 CCTTTTA
19838997 CCTTTTA
1 CCTTTTA
19839004 C
1 C
19839005 TTTCAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.56
Consensus pattern (7 bp):
CCTTTTA
Found at i:19852351 original size:18 final size:19
Alignment explanation
Indices: 19852313--19852351 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
19852303 GGAACTGATA
* *
19852313 CATAAAATTTTATAATGTT
1 CATAAAATTTTAAAATATT
19852332 CATAAAA-TTTAAAATATT
1 CATAAAATTTTAAAATATT
19852350 CA
1 CA
19852352 ATGAGCGCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (19 bp):
CATAAAATTTTAAAATATT
Found at i:19871478 original size:44 final size:44
Alignment explanation
Indices: 19871413--19871677 Score: 180
Period size: 44 Copynumber: 5.8 Consensus size: 44
19871403 GGAAATGGTG
* * *
19871413 AATCTTATCTCCCTGATATTACAGTGGAGCAGATTGAAGCCAGA
1 AATCTTATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTAGA
* * *
19871457 AATCTTATCTCCATGAGATTACAGCGAAGCAGATTGAAGCTAGT
1 AATCTTATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTAGA
* * * **
19871501 AATCCTATCTCCTTGAGGTTACAGTGGAGCAGATT-AAAATA-A
1 AATCTTATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTAGA
*
19871543 AGGATCTTATCTCTC-TGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
1 A--ATCTTATCTC-CATGAGA-TTACAGT---G--GA--G---CAGATTGAAGCTAGA
* ** * *
19871599 AATCTTATCTCCCTGAGATTACAACGGAGCAGATTTAAGCTAGT
1 AATCTTATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTAGA
* * *
19871643 AATCCTATCTCCCA-AAGGTTACAGTGGAGCAGATT
1 AATCTTATCT-CCATGAGATTACAGTGGAGCAGATT
19871678 AAAATAAAGG
Statistics
Matches: 172, Mismatches: 30, Indels: 38
0.72 0.12 0.16
Matches are distributed among these distances:
42 1 0.01
43 4 0.02
44 125 0.73
45 3 0.02
47 2 0.01
49 4 0.02
51 2 0.01
53 1 0.01
54 24 0.14
55 4 0.02
56 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTAGA
Found at i:19871630 original size:142 final size:142
Alignment explanation
Indices: 19871442--19871752 Score: 516
Period size: 142 Copynumber: 2.2 Consensus size: 142
19871432 TACAGTGGAG
* *
19871442 CAGATTGAAGCCAGAAATCTTATCTCCATGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGAAGCAGATTGAAGCTAGTAATCCT
***
19871507 ATCTCCTTGAGGTTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCAAAGGTTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
19871572 AGTAGATCGCAT
131 AGTAGATCGCAT
* *
19871584 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTTAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGAAGCAGATTGAAGCTAGTAATCCT
*
19871649 ATCTCCCAAAGGTTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGACGTTACAGTAG
66 ATCTCCCAAAGGTTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
19871714 AGTAGATCGTAT
131 AGTAGATCGCAT
* *
19871726 TAGATTGAAGCCAGGAATCTTA-CTCCC
1 CAGATTGAAGCCAGAAATCTTATCTCCC
19871753 CAAGCGGTGC
Statistics
Matches: 158, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
141 5 0.03
142 153 0.97
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGAAGCAGATTGAAGCTAGTAATCCT
ATCTCCCAAAGGTTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCGCAT
Found at i:19881696 original size:57 final size:57
Alignment explanation
Indices: 19881626--19881778 Score: 209
Period size: 57 Copynumber: 2.7 Consensus size: 57
19881616 AGAGTTTTGG
* *
19881626 CACAAAGGTTTACCCTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAACAAGTTCAC
1 CACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAACAAGTTCAC
* * * *
19881683 CACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
1 CACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAACAAGTTCAC
* * *
19881740 TACAAAGACTTACCTTTCCT-GAGTTTTTCCACAAAGGCT
1 CACAAAGGCTTACCTTT-CTAGAGTTTTGCCACAAAGGCT
19881779 TATCTTTCCA
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
57 83 0.98
58 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (57 bp):
CACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAACAAGTTCAC
Found at i:19881698 original size:28 final size:28
Alignment explanation
Indices: 19881654--19881756 Score: 77
Period size: 28 Copynumber: 3.6 Consensus size: 28
19881644 TAGAGTTTTG
19881654 CCACAAAGGCTGT-CCTTTAACAAGTTCA
1 CCACAAAGGCT-TACCTTTAACAAGTTCA
**
19881682 CCACAAAGGCTTACCTTT--CTAGAGTTTTG
1 CCACAAAGGCTTACCTTTAAC-A-AG-TTCA
* * * *
19881711 CCACAAAGGTTTTCCTTTAATAGGTTCA
1 CCACAAAGGCTTACCTTTAACAAGTTCA
* *
19881739 CTACAAAGACTTACCTTT
1 CCACAAAGGCTTACCTTT
19881757 CCTGAGTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
26 1 0.02
27 2 0.04
28 34 0.60
29 19 0.33
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (28 bp):
CCACAAAGGCTTACCTTTAACAAGTTCA
Found at i:19881706 original size:86 final size:85
Alignment explanation
Indices: 19881554--19881722 Score: 212
Period size: 86 Copynumber: 2.0 Consensus size: 85
19881544 TAAGGTCTTT
* * * * * *
19881554 CCTTTTAGAGTCTTGCCACAAAGCCATCATTTAAGAGGTTCATCGCAAAGGTTTACCCTTCCAGA
1 CCTTCTAGAGTCTTGCCACAAAGCCATCATTTAACAAGTTCACCACAAAGGCTTACCCTTCCAGA
*
19881619 GTTTTGGCACAAAGGTTTAC
66 GTTTTGCCACAAAGGTTTAC
* ** * * *
19881639 CCTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAACAAGTTCACCACAAAGGCTTACCTTTCTAG
1 CCTTCTAGAGTCTTGCCACAAA-GCCATCATTTAACAAGTTCACCACAAAGGCTTACCCTTCCAG
19881704 AGTTTTGCCACAAAGGTTT
65 AGTTTTGCCACAAAGGTTT
19881723 TCCTTTAATA
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
85 20 0.29
86 50 0.71
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (85 bp):
CCTTCTAGAGTCTTGCCACAAAGCCATCATTTAACAAGTTCACCACAAAGGCTTACCCTTCCAGA
GTTTTGCCACAAAGGTTTAC
Found at i:19881727 original size:29 final size:29
Alignment explanation
Indices: 19881599--19881728 Score: 124
Period size: 29 Copynumber: 4.5 Consensus size: 29
19881589 AGGTTCATCG
* * *
19881599 CAAAGGTTTACCCTTCCAGAGTTTTGGCA
1 CAAAGGTTTACCTTTCTAGAGTTTTGCCA
*
19881628 CAAAGGTTTACCCTTCTAGAGTTTTGCCA
1 CAAAGGTTTACCTTTCTAGAGTTTTGCCA
* **
19881657 CAAAGGCTGT-CCTTTAAC-A-AG-TTCACCA
1 CAAAGG-TTTACCTTT--CTAGAGTTTTGCCA
*
19881685 CAAAGGCTTACCTTTCTAGAGTTTTGCCA
1 CAAAGGTTTACCTTTCTAGAGTTTTGCCA
*
19881714 CAAAGGTTTTCCTTT
1 CAAAGGTTTACCTTT
19881729 AATAGGTTCA
Statistics
Matches: 82, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
26 1 0.01
27 2 0.02
28 18 0.22
29 57 0.70
30 3 0.04
31 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (29 bp):
CAAAGGTTTACCTTTCTAGAGTTTTGCCA
Found at i:19902261 original size:66 final size:66
Alignment explanation
Indices: 19902180--19902324 Score: 227
Period size: 66 Copynumber: 2.2 Consensus size: 66
19902170 GGAATGTCGA
* * * *
19902180 AGTTTTGTTATGTTGGTGTATAGTATTTTCCTATGTGACACACCCTTGGCATATTGAGTTTGTCA
1 AGTTTTGTTATGTTGGTGTATAGTATTTGCCCATGTGACACACCATTGGCATACTGAGTTTGTCA
*
19902245 G
66 C
*
19902246 AGTTTTGTTATGTTGGTGTATAGTATTTGCCCATGTGACACACCATTGGCATACTGAGTTTGTCT
1 AGTTTTGTTATGTTGGTGTATAGTATTTGCCCATGTGACACACCATTGGCATACTGAGTTTGTCA
19902311 C
66 C
19902312 AGTTTTGTATATG
1 AGTTTTGT-TATG
19902325 CCATTAGGCA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
66 68 0.94
67 4 0.06
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (66 bp):
AGTTTTGTTATGTTGGTGTATAGTATTTGCCCATGTGACACACCATTGGCATACTGAGTTTGTCA
C
Found at i:19908442 original size:28 final size:29
Alignment explanation
Indices: 19908387--19908451 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
19908377 ATTTTGCTTC
19908387 AATATAAAAATATATGTAGTGTATTTTAAA
1 AATA-AAAAATATATGTAGTGTATTTTAAA
19908417 AATAAAAAATATATGTAGTGTA-TTTAAA
1 AATAAAAAATATATGTAGTGTATTTTAAA
19908445 AA-AAAAA
1 AATAAAAA
19908452 TTTAATCTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 5 0.14
28 8 0.23
29 18 0.51
30 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (29 bp):
AATAAAAAATATATGTAGTGTATTTTAAA
Found at i:19914940 original size:68 final size:67
Alignment explanation
Indices: 19914868--19915053 Score: 216
Period size: 68 Copynumber: 2.7 Consensus size: 67
19914858 ATATAGTCTT
*
19914868 CCAGGACATTAAACATGGGGTTATAATATGTAAGACCATAGCTCGGA-TATGACAA-CATAGAGA
1 CCAGGACATTAAACATGGGGTTACAA-ATGTAAGACCATAGCTC-GACTATGACAACCA-AGAGA
19914931 GTT-TG
63 -TTCTG
* * * * *
19914936 CCAGGATATTAAACATGGGGTTACAAGTGTAAGACCATATCTCGACTATGATAACCAATAGATTC
1 CCAGGACATTAAACATGGGGTTACAAATGTAAGACCATAGCTCGACTATGACAACCAAGAGATTC
19915001 TG
66 TG
* ** *
19915003 CCAGGACATTAAACATGGAGGTTACAAGTGTAAGAATATAGCTTGACTATG
1 CCAGGACATTAAACATGG-GGTTACAAATGTAAGACCATAGCTCGACTATG
19915054 GAAACTAATA
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
66 4 0.04
67 45 0.44
68 54 0.52
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (67 bp):
CCAGGACATTAAACATGGGGTTACAAATGTAAGACCATAGCTCGACTATGACAACCAAGAGATTC
TG
Found at i:19915005 original size:67 final size:67
Alignment explanation
Indices: 19914868--19915037 Score: 220
Period size: 67 Copynumber: 2.5 Consensus size: 67
19914858 ATATAGTCTT
* *
19914868 CCAGGACATTAAACATGGGGTTATAATATGTAAGACCATAGCTCGGATATGACAACATAGAGAGT
1 CCAGGACATTAAACATGGGGTTACAA-GTGTAAGACCATAGCTCGGATATGACAACATAGAGAGT
19914933 TTG
65 TTG
* * * *
19914936 CCAGGATATTAAACATGGGGTTACAAGTGTAAGACCATATCTC-GACTATGATAACCA-ATAGA-
1 CCAGGACATTAAACATGGGGTTACAAGTGTAAGACCATAGCTCGGA-TATGACAA-CATAGAGAG
19914998 TTCTG
64 TT-TG
19915003 CCAGGACATTAAACATGGAGGTTACAAGTGTAAGA
1 CCAGGACATTAAACATGG-GGTTACAAGTGTAAGA
19915038 ATATAGCTTG
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
66 4 0.04
67 45 0.49
68 42 0.46
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (67 bp):
CCAGGACATTAAACATGGGGTTACAAGTGTAAGACCATAGCTCGGATATGACAACATAGAGAGTT
TG
Found at i:19915080 original size:68 final size:68
Alignment explanation
Indices: 19914868--19915105 Score: 188
Period size: 68 Copynumber: 3.5 Consensus size: 68
19914858 ATATAGTCTT
* * * * * *
19914868 CCAGGACATTAAACATGG-GGTTATAATATGTAAGACCATAGCTCGGA-TATGACAA-CATAGAG
1 CCAGAACATTAAACATGGAGGTTACAA-GTGTAAGAACATAGCTC-GACTATGATAACCA-ATAG
19914930 AGTT-TG
63 A-TTCTG
* * * *
19914936 CCAGGATATTAAACATGG-GGTTACAAGTGTAAGACCATATCTCGACTATGATAACCAATAGATT
1 CCAGAACATTAAACATGGAGGTTACAAGTGTAAGAACATAGCTCGACTATGATAACCAATAGATT
19915000 CTG
66 CTG
* * * * *
19915003 CCAGGACATTAAACATGGAGGTTACAAGTGTAAGAATATAGCTTGACTATGGA-AACTAATA-AA
1 CCAGAACATTAAACATGGAGGTTACAAGTGTAAGAACATAGCTCGACTAT-GATAACCAATAGAT
*
19915066 GCTTG
65 TC-TG
*
19915071 TCCA-AACATTAAACAT-GAGATTACAATGTGTAAGA
1 -CCAGAACATTAAACATGGAGGTTACAA-GTGTAAGA
19915106 CCATGGATCG
Statistics
Matches: 146, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
66 4 0.03
67 56 0.38
68 81 0.55
69 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (68 bp):
CCAGAACATTAAACATGGAGGTTACAAGTGTAAGAACATAGCTCGACTATGATAACCAATAGATT
CTG
Found at i:19917395 original size:112 final size:112
Alignment explanation
Indices: 19917169--19917384 Score: 260
Period size: 112 Copynumber: 1.9 Consensus size: 112
19917159 AGATCTGACG
* * * *
19917169 ACCAAAACGCATTGTTTTG-GTCTTGATGTATACTAGAATTAGTGGCGTTTATGATAAAACGCCG
1 ACCAAAATGCATCGTTTTGTGTC--GTTGTATACTAGAATTAGTGGCGTTTACGATAAAACGCCG
* * **
19917233 CTAAAGGAAGTATTAGCGGCGCATTGTCGCAAGCGCCGCAAAAACCTTA
64 CTAAAGCAAGTATTAGCGGCGCATTCTCAAAAGCGCCGCAAAAACCTTA
* * * *
19917282 ACGAAAATGCATCGTTTTGTGTCGTTGTATATTAGCATTAGTGGCGTTTACGA-AAACCCGCCGC
1 ACCAAAATGCATCGTTTTGTGTCGTTGTATACTAGAATTAGTGGCGTTTACGATAAA-ACGCCGC
19917346 TAAAGCAAGTATTAGCGGCGC-TTACT-AAAAGCGCCGCAA
65 TAAAGCAAGTATTAGCGGCGCATT-CTCAAAAGCGCCGCAA
19917385 TATATGTTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
111 16 0.18
112 53 0.60
113 16 0.18
114 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (112 bp):
ACCAAAATGCATCGTTTTGTGTCGTTGTATACTAGAATTAGTGGCGTTTACGATAAAACGCCGCT
AAAGCAAGTATTAGCGGCGCATTCTCAAAAGCGCCGCAAAAACCTTA
Found at i:19918046 original size:229 final size:226
Alignment explanation
Indices: 19917524--19918058 Score: 540
Period size: 229 Copynumber: 2.3 Consensus size: 226
19917514 CGTTTAAGGG
* * * * * * *
19917524 AAAACGCCGCTAAAGCATAATATTAGGGGCGTTTTGTGTGAAGCACCGCAAAATATCTTAACCAA
1 AAAACACCGCTAAAGCATAGTATTAGCGGCCTTTT-TGAGAAACGCCGCAAAATATCTTAACCAA
* * * *
19917589 AATGCAGAGTTTGGTCATGAGGTATACTAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAGGCA
65 AACGCAGAGTTTTGTCATCAGGTATACTAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAAGCA
* * * * **
19917654 TACTATTAGCGGCGCTTTAAGAGAAGCGCCGCAAAATTTGGTAACCAAACGCAACGTTTTTGTCT
130 TACTATTAGCGGCGCTTTAAGAGAAGCGCCACAAAATATAGTAACAAAACGCAACGTTTAAGTCT
* * *
19917719 TGATGTATACAGTTATTAGTGGCAAATATTAA
195 TGATGTATACAGTAATTAGTGGCAAACACTAA
* * * * *
19917751 AAAACACCGCTAAATCATAGTATTAGCGGCGC--TTGGCAAAAAGCGCCGCAACATATGC-TCAC
1 AAAACACCGCTAAAGCATAGTATTAGCGGC-CTTTTTG-AGAAA-CGCCGCAAAATAT-CTTAAC
* * * * *
19917813 CAAAACGCAGAGTTTTTTCATCAGGTATATTAGAATTAGTGGCGCTTATGGGAGA-ACGCCGTTA
62 CAAAACGCAGAGTTTTGTCATCAGGTATACTAGAATTAGTGGCGC-AAAGGGA-ACACGCCGCTA
** * * **
19917877 AAGCATACTATTAGCGGCGCTTTTTGAGAAGTGCCACAAAATATATTAACAAAAACGCAGTGTTT
125 AAGCATACTATTAGCGGCGCTTTAAGAGAAGCGCCACAAAATATAGTAAC-AAAACGCAACGTTT
*** *
19917942 AAGTCTTGATGTATACTAG-AATTAGTGGCGTCCACTAG
189 AAGTCTTGATGTATAC-AGTAATTAGTGGCAAACACTAA
* ** * *
19917980 AAAGCGTCGCTAAAGCATAGTATTAGTGGCACTTTTTGAGAAACGCCGGAAAATATCTTAACCAA
1 AAAACACCGCTAAAGCATAGTATTAGCGGC-CTTTTTGAGAAACGCCGCAAAATATCTTAACCAA
19918045 AACGCAGAGTTTTG
65 AACGCAGAGTTTTG
19918059 GTCTTAACCA
Statistics
Matches: 245, Mismatches: 52, Indels: 20
0.77 0.16 0.06
Matches are distributed among these distances:
225 1 0.00
226 4 0.02
227 80 0.33
228 57 0.23
229 94 0.38
230 6 0.02
231 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (226 bp):
AAAACACCGCTAAAGCATAGTATTAGCGGCCTTTTTGAGAAACGCCGCAAAATATCTTAACCAAA
ACGCAGAGTTTTGTCATCAGGTATACTAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAAGCAT
ACTATTAGCGGCGCTTTAAGAGAAGCGCCACAAAATATAGTAACAAAACGCAACGTTTAAGTCTT
GATGTATACAGTAATTAGTGGCAAACACTAA
Found at i:19918063 original size:115 final size:113
Alignment explanation
Indices: 19917449--19918063 Score: 447
Period size: 114 Copynumber: 5.4 Consensus size: 113
19917439 GCTTATGGGA
* ** ** * ** *
19917449 AAACGCCGCAAAATATCCTAACCAAAGTGCACCGTTTTGGTCTTGGTGTATGTTACAATTAGTGG
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGG
* * * * *
19917514 CGTTTAAGGGAAAACGCCGCTAAAGCATAATATTAGGGGCG-TTTTGTGTG
66 CG-CTAATGG-AAACGCCGCTAAAGCATACTATTAGCGGCGCTTTT-TGAG
* * * * *
19917564 AAGCACCGCAAAATATCTTAACCAAAATGCAGAG-TTTGGTCATGAGGTATACTAGAATTAGTGG
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGG
* * * **
19917628 CGCAAAGGGAACACGCCGCTAAGGCATACTATTAGCGGCGCTTTAAGAG
66 CGCTAATGGAA-ACGCCGCTAAAGCATACTATTAGCGGCGCTTTTTGAG
* * ** * *
19917677 AAGCGCCGCAAAATTTGGTAACC-AAACGCA-ACGTTTTTGTCTTGATGTATAC-AGTTATTAGT
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGA-GTTTTGGTCTTGATGTATACTAG-AATTAGT
** * ** * * * * *
19917739 GGCAAATATTAAAAAACACCGCTAAATCATAGTATTAGCGGCGC--TTGGCAA
64 GGC-GCTAAT-GGAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTTTG-AG
* * * * * * *
19917790 AAAGCGCCGCAACATATGC-TCACCAAAACGCAGAGTTTT-TTCATCAGGTATATTAGAATTAGT
1 AAA-CGCCGCAAAATAT-CTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGT
* *
19917853 GGCGCTTATGGGAGAACGCCGTTAAAGCATACTATTAGCGGCGCTTTTTGAG
64 GGCGCTAAT-GGA-AACGCCGCTAAAGCATACTATTAGCGGCGCTTTTTGAG
** * * * * **
19917905 AAGTGCCACAAAATATATTAACAAAAACGCAGTGTTTAAGTCTTGATGTATACTAGAATTAGTGG
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGG
* * * * * * *
19917970 CGTCCACTAGAAAGCGTCGCTAAAGCATAGTATTAGTGGCACTTTTTGAG
66 CG-CTAATGGAAA-CGCCGCTAAAGCATACTATTAGCGGCGCTTTTTGAG
*
19918020 AAACGCCGGAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
19918064 AACCATGCAT
Statistics
Matches: 381, Mismatches: 99, Indels: 40
0.73 0.19 0.08
Matches are distributed among these distances:
111 1 0.00
112 13 0.03
113 81 0.21
114 142 0.37
115 138 0.36
116 6 0.02
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (113 bp):
AAACGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGG
CGCTAATGGAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTTTGAG
Found at i:19919508 original size:41 final size:40
Alignment explanation
Indices: 19919437--19919516 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
19919427 GATTACAACT
19919437 TTAACAATTAGCGGCGATTTTACTAAAAACGCCGCTAAAAA
1 TTAACAATTAGCGGCGATTTTACTAAAAACGCCGC-AAAAA
19919478 TTAAGCAA-TAGCGGCG-TTTGTAC-AAGAAACGCCGCAAAA
1 TTAA-CAATTAGCGGCGATTT-TACTAA-AAACGCCGCAAAA
19919517 GTGAGTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
40 9 0.25
41 24 0.67
42 3 0.08
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (40 bp):
TTAACAATTAGCGGCGATTTTACTAAAAACGCCGCAAAAA
Found at i:19922689 original size:27 final size:27
Alignment explanation
Indices: 19922651--19923065 Score: 614
Period size: 27 Copynumber: 15.4 Consensus size: 27
19922641 CTTACATTAA
*
19922651 TTACATAACTTACAAAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
19922678 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
19922705 TTACATAACTTATAAAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
19922732 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
*
19922759 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
*
19922786 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
*
19922813 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
19922840 TTACATAACTTACATAAATTAAGTAAA
1 TTACATAACTTACATAAATTAAATAAC
*
19922867 TTAAATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
19922894 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
19922921 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* *
19922948 TTATATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
* * * *
19922975 TTACATAACTTAAATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
* *
19923002 TTAAATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
* * *
19923029 TTACATAACTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
*
19923056 TTAAATAACT
1 TTACATAACT
19923066 GGCATAACTT
Statistics
Matches: 351, Mismatches: 37, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 351 1.00
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.34
Consensus pattern (27 bp):
TTACATAACTTACATAAATTAAATAAC
Found at i:19923072 original size:18 final size:18
Alignment explanation
Indices: 19922630--19923065 Score: 410
Period size: 18 Copynumber: 24.7 Consensus size: 18
19922620 TAGGTATCAC
19922630 AAATTAAATAACTTACAT
1 AAATTAAATAACTTACAT
* * *
19922648 TAATTACATAACTTACAA
1 AAATTAAATAACTTACAT
19922666 AAATTAAATAACTTACAT
1 AAATTAAATAACTTACAT
* * *
19922684 AACTTACATAAATTA-AGT
1 AAATTAAATAACTTACA-T
* * * *
19922702 AACTTACATAACTTATAA
1 AAATTAAATAACTTACAT
19922720 AAATTAAATAACTTACAT
1 AAATTAAATAACTTACAT
* * * *
19922738 AACTTACATAAATTAAAT
1 AAATTAAATAACTTACAT
** *
19922756 ATCTTACATAACTTACAT
1 AAATTAAATAACTTACAT
*
19922774 AAATTAAGTAACTTACAT
1 AAATTAAATAACTTACAT
* * *
19922792 AACTTACATAAATTA-AGT
1 AAATTAAATAACTTACA-T
* *
19922810 AACTTACATAACTTACAT
1 AAATTAAATAACTTACAT
*
19922828 AAATTAAGTAACTTACAT
1 AAATTAAATAACTTACAT
* * *
19922846 AACTTACATAAATTA-AGT
1 AAATTAAATAACTTACA-T
19922864 AAATTAAATAACTTACAT
1 AAATTAAATAACTTACAT
19922882 AAATTAAATAACTTAC--
1 AAATTAAATAACTTACAT
19922898 -------ATAACTTACAT
1 AAATTAAATAACTTACAT
19922909 AAATTAAATAACTTACAT
1 AAATTAAATAACTTACAT
* * * *
19922927 AACTTACATAAATTAAAT
1 AAATTAAATAACTTACAT
** *
19922945 ATCTTATATAACTTACAT
1 AAATTAAATAACTTACAT
*
19922963 AAATTAAGTAACTTACAT
1 AAATTAAATAACTTACAT
*
19922981 AACTTAAATAACTTACAT
1 AAATTAAATAACTTACAT
19922999 AAATTAAATAACTTACAT
1 AAATTAAATAACTTACAT
*
19923017 AAATTAAGTAACTTACAT
1 AAATTAAATAACTTACAT
* *
19923035 AACTTACATAACTTACAT
1 AAATTAAATAACTTACAT
19923053 AAATTAAATAACT
1 AAATTAAATAACT
19923066 GGCATAACTT
Statistics
Matches: 341, Mismatches: 62, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
9 9 0.03
17 3 0.01
18 326 0.96
19 3 0.01
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.34
Consensus pattern (18 bp):
AAATTAAATAACTTACAT
Found at i:19923123 original size:25 final size:25
Alignment explanation
Indices: 19923068--19923123 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
19923058 AAATAACTGG
* *
19923068 CATAACTTACATTATACATAACCTT
1 CATAACTTACATTATACACAACCTA
*
19923093 CTTAACTTACATTATACACAA-CTCA
1 CATAACTTACATTATACACAACCT-A
19923118 CATAAC
1 CATAAC
19923124 GATGTAGTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (25 bp):
CATAACTTACATTATACACAACCTA
Found at i:19923196 original size:7 final size:7
Alignment explanation
Indices: 19923184--19923237 Score: 72
Period size: 7 Copynumber: 7.1 Consensus size: 7
19923174 TACATGGGGC
19923184 ATACATA
1 ATACATA
19923191 ATACATA
1 ATACATA
19923198 ATACATA
1 ATACATA
19923205 ATACATA
1 ATACATA
19923212 ACTTACATA
1 A--TACATA
19923221 ACTTACATA
1 A--TACATA
19923230 ATACATA
1 ATACATA
19923237 A
1 A
19923238 AAATATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
7 29 0.64
9 16 0.36
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.30
Consensus pattern (7 bp):
ATACATA
Found at i:19923211 original size:25 final size:24
Alignment explanation
Indices: 19923185--19923237 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
19923175 ACATGGGGCA
19923185 TACATAATACATAA--TACATAA-
1 TACATAATACATAACTTACATAAC
19923206 TACATAACTTACATAACTTACATAA-
1 TACATAA--TACATAACTTACATAAC
19923231 TACATAA
1 TACATAA
19923238 AAATATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.25
23 7 0.25
25 14 0.50
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (24 bp):
TACATAATACATAACTTACATAAC
Found at i:19929311 original size:42 final size:42
Alignment explanation
Indices: 19929258--19929387 Score: 143
Period size: 42 Copynumber: 3.1 Consensus size: 42
19929248 TAGTGGCGTT
* * *
19929258 TTTGTAAAAAAGTGCCGCTAAAGAACATGTTCTGTAGCGGCG
1 TTTGTAAAAAAGCGCCGCTAAAGAACATGATCTCTAGCGGCG
* ** *
19929300 TTTGTAAAAAAGCGCCGCTAAATATTATGATCTCTAGCGGAG
1 TTTGTAAAAAAGCGCCGCTAAAGAACATGATCTCTAGCGGCG
* * * * *
19929342 TTTTTATACAAAGCGCCGTTAAAGAACATGATCTTTAGTGGCG
1 TTTGTA-AAAAAGCGCCGCTAAAGAACATGATCTCTAGCGGCG
19929385 TTT
1 TTT
19929388 TTGGTTGTAA
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 40 0.56
43 31 0.44
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (42 bp):
TTTGTAAAAAAGCGCCGCTAAAGAACATGATCTCTAGCGGCG
Found at i:19930342 original size:12 final size:13
Alignment explanation
Indices: 19930325--19930358 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
19930315 AAAGAAGGAG
19930325 AAATGGAAA-AAA
1 AAATGGAAATAAA
19930337 AAATGGAGAATAAA
1 AAATGGA-AATAAA
19930351 AAATGGAA
1 AAATGGAA
19930359 GCAACTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 3 0.15
14 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.12
Consensus pattern (13 bp):
AAATGGAAATAAA
Found at i:19932685 original size:43 final size:43
Alignment explanation
Indices: 19932618--19932740 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 43
19932608 TTTTCAAAAA
* *
19932618 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGTATCGA-CTT
1 GTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCATCGATC-T
*
19932661 GTGTTTTTATGTAAGACC-CTGTCTGGGACAG-TGGCATCGATCT
1 GTGTTTTCATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATCT
* *
19932704 GTGTTTACATGTAAGACCACGTCTAGGACGTTGGCAT
1 GTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCAT
19932741 TGTACAAGCC
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 2 0.03
43 64 0.93
44 3 0.04
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (43 bp):
GTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCATCGATCT
Found at i:19932973 original size:28 final size:29
Alignment explanation
Indices: 19932917--19932973 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
19932907 TTAAATTATA
*
19932917 AATGTGAACTATGTGTATACATATGTGGT
1 AATGTGAACTATGTGTATACAAATGTGGT
* * *
19932946 AATGT-AATTATGTGTATGCAAATTTGGT
1 AATGTGAACTATGTGTATACAAATGTGGT
19932974 GATGCATAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (29 bp):
AATGTGAACTATGTGTATACAAATGTGGT
Found at i:19935229 original size:19 final size:18
Alignment explanation
Indices: 19935207--19935245 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19935197 AATATAATAT
19935207 AAAACAAATAAATAAAAGA
1 AAAACAAAT-AATAAAAGA
* *
19935226 AAAAGAAATAGTAAAAGA
1 AAAACAAATAATAAAAGA
19935244 AA
1 AA
19935246 CAAGATAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAACAAATAATAAAAGA
Found at i:19935277 original size:13 final size:12
Alignment explanation
Indices: 19935259--19935296 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
19935249 GATAGAAACG
19935259 AAACAGAAAGGAA
1 AAACAGAAA-GAA
19935272 AAACAGAAAGAA
1 AAACAGAAAGAA
*
19935284 AAA-GGAAAGAA
1 AAACAGAAAGAA
19935295 AA
1 AA
19935297 GGAGAAAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 9 0.38
12 6 0.25
13 9 0.38
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (12 bp):
AAACAGAAAGAA
Found at i:19936295 original size:40 final size:40
Alignment explanation
Indices: 19936174--19936313 Score: 137
Period size: 40 Copynumber: 3.5 Consensus size: 40
19936164 GACTTTGAGT
* *
19936174 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTTATT
1 CGATGAGACACTAGGTGTCAAATTATTACTTC-GATTTATC
* * * * * *
19936215 CGATGAGGCAGTAGGTG-CCAA--GTTACTTCGGTTTAGC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGATTTATC
*
19936252 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGATTTATC
19936292 CGATGATG-CACT-GGCTGTCAAA
1 CGATGA-GACACTAGG-TGTCAAA
19936314 CTGGTGTGTT
Statistics
Matches: 79, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
37 20 0.25
38 10 0.13
39 2 0.03
40 32 0.41
41 15 0.19
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTAGGTGTCAAATTATTACTTCGATTTATC
Found at i:19939891 original size:24 final size:26
Alignment explanation
Indices: 19939864--19939915 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
19939854 CTCGTTAAGT
19939864 GCTCTTTG-GAGCTACCCGATA-TAA
1 GCTCTTTGTGAGCTACCCGATATTAA
* *
19939888 GCTCTTTGTGAGCTTCCCGTTATTAA
1 GCTCTTTGTGAGCTACCCGATATTAA
19939914 GC
1 GC
19939916 CCAGATAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 11 0.46
26 5 0.21
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (26 bp):
GCTCTTTGTGAGCTACCCGATATTAA
Found at i:19948263 original size:19 final size:21
Alignment explanation
Indices: 19948209--19948267 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
19948199 TGAAAATTTT
* *
19948209 AATTTTAATTTAATATTTTTATA
1 AATTTTAA--TAATGTTTTTACA
19948232 AATTTTAATAATGTTTTTACA
1 AATTTTAATAATGTTTTTACA
19948253 AA-TTT-ATAATGTTTT
1 AATTTTAATAATGTTTT
19948268 AATTTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.29
20 3 0.09
21 13 0.38
23 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (21 bp):
AATTTTAATAATGTTTTTACA
Found at i:19949700 original size:15 final size:16
Alignment explanation
Indices: 19949660--19949701 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
19949650 TGATTGCGCT
19949660 GGACTTTACAATTTGA
1 GGACTTTACAATTTGA
19949676 GGACTTTACAATATT-A
1 GGACTTTACAAT-TTGA
19949692 GGA-TTTACAA
1 GGACTTTACAA
19949702 GCGAATATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.28
16 16 0.64
17 2 0.08
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (16 bp):
GGACTTTACAATTTGA
Found at i:19950101 original size:18 final size:21
Alignment explanation
Indices: 19950078--19950115 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 21
19950068 AGAACATAAC
19950078 TTACCT-TT-CACA-CCTTCG
1 TTACCTCTTCCACATCCTTCG
19950096 TTACCTCTTCCACATCCTTC
1 TTACCTCTTCCACATCCTTC
19950116 ACCCTACCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 4 0.24
21 5 0.29
ACGTcount: A:0.16, C:0.42, G:0.03, T:0.39
Consensus pattern (21 bp):
TTACCTCTTCCACATCCTTCG
Found at i:19950143 original size:18 final size:17
Alignment explanation
Indices: 19950120--19950153 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
19950110 TCCTTCACCC
19950120 TACCCATTCCTGATTTCT
1 TACCCATTCCT-ATTTCT
19950138 TACCCATTCCTATTTC
1 TACCCATTCCTATTTC
19950154 GAAAAACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.18, C:0.35, G:0.03, T:0.44
Consensus pattern (17 bp):
TACCCATTCCTATTTCT
Found at i:19950371 original size:54 final size:55
Alignment explanation
Indices: 19950312--19950433 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 55
19950302 AAGCCTTTCT
* * * * * **
19950312 TTCAGAGTTCT-CCGTACACATTACTCTTTTAGAGTTCACCATATTTACTGTGCC
1 TTCAGAGTTCTGCCATACACATTACTCCTTCAAAGTTCACCATACTTACTGCACC
* * *
19950366 TTCAGA-TTTTGCCATACATATTATTCCTTCAAAGTTCACCATACTTACTGCACC
1 TTCAGAGTTCTGCCATACACATTACTCCTTCAAAGTTCACCATACTTACTGCACC
19950420 TTCAGAGTTC-GCCA
1 TTCAGAGTTCTGCCA
19950434 GGAATACCAT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
53 3 0.05
54 50 0.91
55 2 0.04
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (55 bp):
TTCAGAGTTCTGCCATACACATTACTCCTTCAAAGTTCACCATACTTACTGCACC
Found at i:19950615 original size:26 final size:26
Alignment explanation
Indices: 19950570--19950695 Score: 153
Period size: 26 Copynumber: 4.8 Consensus size: 26
19950560 TTCCAAAGAC
* *
19950570 TGCCACAGAGGCTTCCATTTCAGATA
1 TGCCACAAAGGCTTTCATTTCAGATA
* * * *
19950596 TACCACAAAGACTTTAATTTTAGATA
1 TGCCACAAAGGCTTTCATTTCAGATA
* *
19950622 TGGCACAAAGGCTTTCATTTTAGATA
1 TGCCACAAAGGCTTTCATTTCAGATA
*
19950648 TGCCACAAAGGCTTTCATTTCAAATA
1 TGCCACAAAGGCTTTCATTTCAGATA
* *
19950674 CGCCACAAAGGCTTCCATTTCA
1 TGCCACAAAGGCTTTCATTTCA
19950696 TAGATTACCA
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 85 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (26 bp):
TGCCACAAAGGCTTTCATTTCAGATA
Found at i:19957680 original size:11 final size:11
Alignment explanation
Indices: 19957664--19957694 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
19957654 TTTGAATGTG
19957664 ATTTCAAGGAT
1 ATTTCAAGGAT
19957675 ATTTCAAGGAT
1 ATTTCAAGGAT
*
19957686 ACTTCAAGG
1 ATTTCAAGG
19957695 GCTGATTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (11 bp):
ATTTCAAGGAT
Found at i:19972136 original size:15 final size:17
Alignment explanation
Indices: 19972105--19972136 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
19972095 TTCAAACACG
19972105 ATTTAACACATTATCAA
1 ATTTAACACATTATCAA
19972122 ATTT-ACACA-TATCAA
1 ATTTAACACATTATCAA
19972137 CAAAGCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTAACACATTATCAA
Found at i:19985853 original size:17 final size:18
Alignment explanation
Indices: 19985812--19985853 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
19985802 AAAAAACTTG
*
19985812 AAAATAATATATTTATTA
1 AAAATAATATATTAATTA
**
19985830 ATTATAAT-TATTAATTA
1 AAAATAATATATTAATTA
19985847 AAAATAA
1 AAAATAA
19985854 AAAGGAGCCT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATAATATATTAATTA
Found at i:19987804 original size:23 final size:23
Alignment explanation
Indices: 19987776--19987821 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
19987766 ATGAGTTAGA
*
19987776 GTTTGTGCACCTTAGTTAGTATG
1 GTTTGTGCACCTTAGTCAGTATG
*
19987799 GTTTGTGCGCCTTAGTCAGTATG
1 GTTTGTGCACCTTAGTCAGTATG
19987822 CGCCTGAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.41
Consensus pattern (23 bp):
GTTTGTGCACCTTAGTCAGTATG
Found at i:19989602 original size:30 final size:31
Alignment explanation
Indices: 19989545--19989603 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
19989535 AGAAAGAAAG
* ***
19989545 AAGGAGCTGAAAGTAAGCTCGGTTGAGCTCA
1 AAGGAGCTGAAAGCAAGCTCAAATGAGCTCA
19989576 AAGGAGCTGAAA-CAAGCTCAAATGAGCT
1 AAGGAGCTGAAAGCAAGCTCAAATGAGCT
19989604 GAGTTGAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (31 bp):
AAGGAGCTGAAAGCAAGCTCAAATGAGCTCA
Found at i:19989613 original size:20 final size:20
Alignment explanation
Indices: 19989566--19989613 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
19989556 AGTAAGCTCG
19989566 GTTGAGCTCAAAGGAGCTGA
1 GTTGAGCTCAAAGGAGCTGA
**** *
19989586 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAAGGAGCTGA
19989606 GTTGAGCT
1 GTTGAGCT
19989614 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAAGGAGCTGA
Found at i:19991340 original size:48 final size:48
Alignment explanation
Indices: 19991285--19991390 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
19991275 TTGTCTTTTC
*
19991285 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
19991333 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
19991381 TTTCTTTTTC
1 TTTCTTTTTC
19991391 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:19994054 original size:25 final size:25
Alignment explanation
Indices: 19994026--19994104 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
19994016 CTAATGGCCG
19994026 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
19994051 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
19994073 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
19994098 ATGTGAT
1 ATGTGAT
19994105 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:19994076 original size:47 final size:47
Alignment explanation
Indices: 19994010--19994577 Score: 1003
Period size: 47 Copynumber: 12.1 Consensus size: 47
19994000 GAAATGATAG
19994010 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
19994057 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
19994104 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
19994151 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
19994198 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
19994245 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
19994292 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
19994339 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
19994386 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
19994433 TAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
19994480 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * *
19994527 CGGGGCC-AAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAA-TGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
19994574 TAAG
1 TAAG
19994578 TCCCGAAGGG
Statistics
Matches: 499, Mismatches: 21, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
46 2 0.00
47 497 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:19994752 original size:37 final size:37
Alignment explanation
Indices: 19994696--19994774 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
19994686 CCGAGCTCTA
* *
19994696 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
19994733 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
19994770 AAGAC
1 AAGAC
19994775 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:19996844 original size:13 final size:13
Alignment explanation
Indices: 19996826--19996858 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
19996816 TATACTTCGA
19996826 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
19996839 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
19996852 TTTTTTT
1 TTTTTTT
19996859 CAAATTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:19998415 original size:30 final size:31
Alignment explanation
Indices: 19998358--19998416 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
19998348 AGAAAGAAAG
* ***
19998358 AAGGAGCTGAAAGTAAGCTCGGTTGAGCTCA
1 AAGGAGCTGAAAGCAAGCTCAAATGAGCTCA
19998389 AAGGAGCTGAAA-CAAGCTCAAATGAGCT
1 AAGGAGCTGAAAGCAAGCTCAAATGAGCT
19998417 GAGTTGAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (31 bp):
AAGGAGCTGAAAGCAAGCTCAAATGAGCTCA
Found at i:19998426 original size:20 final size:20
Alignment explanation
Indices: 19998379--19998426 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
19998369 AGTAAGCTCG
19998379 GTTGAGCTCAAAGGAGCTGA
1 GTTGAGCTCAAAGGAGCTGA
**** *
19998399 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAAGGAGCTGA
19998419 GTTGAGCT
1 GTTGAGCT
19998427 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAAGGAGCTGA
Found at i:20001953 original size:31 final size:31
Alignment explanation
Indices: 20001918--20001979 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
20001908 ATGGAGGACA
20001918 TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
1 TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
20001949 TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
1 TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
20001980 GACTTCTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.16, C:0.10, G:0.29, T:0.45
Consensus pattern (31 bp):
TCGTAGAGGTGAAGTTGCTATGTTGTTTCTT
Found at i:20002409 original size:22 final size:20
Alignment explanation
Indices: 20002353--20002409 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
20002343 TCAAATATAT
20002353 ATAAACATTAAATATATAAAA
1 ATAAA-ATTAAATATATAAAA
20002374 ATAGAAA-TAAATATATAAAA
1 ATA-AAATTAAATATATAAAA
*
20002394 ATTTAAAATTATATAT
1 A--TAAAATTAAATAT
20002410 TCTAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 14 0.45
21 7 0.23
22 10 0.32
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAATTAAATATATAAAA
Found at i:20003571 original size:32 final size:31
Alignment explanation
Indices: 20003491--20003581 Score: 155
Period size: 31 Copynumber: 2.9 Consensus size: 31
20003481 AATACTCTTA
20003491 TCTTTATAAATTCACTAACCTTGTGAGGTTT
1 TCTTTATAAATTCACTAACCTTGTGAGGTTT
*
20003522 TCTGTATAAATTCACTAACCTTGTGAGGTTT
1 TCTTTATAAATTCACTAACCTTGTGAGGTTT
*
20003553 GTCTTTATAAATTTACTAACCTTGTGAGG
1 -TCTTTATAAATTCACTAACCTTGTGAGG
20003582 CTTGGGGTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 30 0.54
32 26 0.46
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (31 bp):
TCTTTATAAATTCACTAACCTTGTGAGGTTT
Found at i:20011082 original size:20 final size:22
Alignment explanation
Indices: 20011044--20011083 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
20011034 TTTGTTATCG
20011044 TTTTTAAGAAAGATATCGATTA
1 TTTTTAAGAAAGATATCGATTA
20011066 TTTTTAA-AAAG-TATCGAT
1 TTTTTAAGAAAGATATCGAT
20011084 ACCAAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (22 bp):
TTTTTAAGAAAGATATCGATTA
Found at i:20014630 original size:29 final size:31
Alignment explanation
Indices: 20014556--20014630 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
20014546 AACGGCTTAG
* * *
20014556 TGACTAAAATATTACAATGTGATAACATAAG
1 TGACTAAAATATAACAATGTCATAACATAAA
** *
20014587 TGACTAAAACGTAAC-ATTTCA-AACATAAA
1 TGACTAAAATATAACAATGTCATAACATAAA
20014616 TGACTAAAATATAAC
1 TGACTAAAATATAAC
20014631 CTGAGCAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
29 20 0.56
30 4 0.11
31 12 0.33
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (31 bp):
TGACTAAAATATAACAATGTCATAACATAAA
Found at i:20014959 original size:24 final size:23
Alignment explanation
Indices: 20014911--20014960 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
20014901 TAAATTCATA
20014911 ATATTAAATATTAAAAATAGTTTT
1 ATATTAAATATTAAAAATAG-TTT
*
20014935 ATATTAATATATATTAAAATA-TTT
1 ATATTAA-ATAT-TAAAAATAGTTT
20014959 AT
1 AT
20014961 TTTTATTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 12 0.52
25 4 0.17
26 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTAAATATTAAAAATAGTTT
Found at i:20018040 original size:30 final size:31
Alignment explanation
Indices: 20017983--20018042 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
20017973 GCTAGGGTAA
* *
20017983 TTTGGGTAACGAAGTATAGTTTTGGTACCAC
1 TTTGGGTAACGAAGTATAATTTAGGTACCAC
* *
20018014 TTTGGGT-ACGAATTTTAATTTAGGTACCA
1 TTTGGGTAACGAAGTATAATTTAGGTACCA
20018043 TTTATAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (31 bp):
TTTGGGTAACGAAGTATAATTTAGGTACCAC
Found at i:20020921 original size:21 final size:21
Alignment explanation
Indices: 20020895--20020936 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20020885 CTCAGAGTAG
20020895 GATCATCAAATTTTTGTTGCT
1 GATCATCAAATTTTTGTTGCT
20020916 GATCATCAAATTTTTGTTGCT
1 GATCATCAAATTTTTGTTGCT
20020937 TTCGTTGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (21 bp):
GATCATCAAATTTTTGTTGCT
Found at i:20031039 original size:16 final size:16
Alignment explanation
Indices: 20031018--20031048 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20031008 AGGCAAGTTA
20031018 AAGAAATTCAGAAATG
1 AAGAAATTCAGAAATG
20031034 AAGAAATTCAGAAAT
1 AAGAAATTCAGAAAT
20031049 CAAGCCAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (16 bp):
AAGAAATTCAGAAATG
Found at i:20037764 original size:21 final size:21
Alignment explanation
Indices: 20037740--20037785 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
20037730 TCATTGCTCA
*
20037740 ACACATATTTACCAAATCATT
1 ACACAAATTTACCAAATCATT
20037761 ACACAAATTTACCAAATCATT
1 ACACAAATTTACCAAATCATT
20037782 ACAC
1 ACAC
20037786 GACAAATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (21 bp):
ACACAAATTTACCAAATCATT
Found at i:20039958 original size:40 final size:40
Alignment explanation
Indices: 20039874--20040098 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 40
20039864 TTGAATGATG
* * * *
20039874 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * * *
20039914 TCCGGACTAAGAT-CCGAAGGTATTTGTACGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
20039954 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
20039993 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
20040033 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
20040072 TACCCGGCTATGTCCCGAAGGCATTTG
1 T-CCGGGCTAAGTCCCGAAGGCATTTG
20040099 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
39 34 0.22
40 116 0.74
41 7 0.04
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:20040010 original size:79 final size:80
Alignment explanation
Indices: 20039874--20040070 Score: 238
Period size: 79 Copynumber: 2.5 Consensus size: 80
20039864 TTGAATGATG
* * * * * *
20039874 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTAAGATCCGAAGGCAAT
*
20039938 TGTACGAGATACTAAT
65 TGTACGAGATACTAAA
* **
20039954 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT-CCGAAGGCAAT
* *
20040017 TGTGCGAGTTACTAAA
65 TGTACGAGATACTAAA
*
20040033 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
20040071 TTACCCGGCT
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
79 57 0.57
80 42 0.42
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCAATT
GTACGAGATACTAAA
Found at i:20058748 original size:12 final size:12
Alignment explanation
Indices: 20058731--20058771 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
20058721 AATAAGCTCA
*
20058731 TTTATTGGCTTG
1 TTTATTGACTTG
*
20058743 TTTATTGACTCG
1 TTTATTGACTTG
20058755 TTTA-TGACTTG
1 TTTATTGACTTG
20058766 TTTATT
1 TTTATT
20058772 TATTAATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.59
Consensus pattern (12 bp):
TTTATTGACTTG
Found at i:20063980 original size:19 final size:21
Alignment explanation
Indices: 20063956--20064002 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
20063946 TTAAGTATAA
*
20063956 TATAAAT-T-TCAAATATTGT
1 TATAAATATCTCAAATATTAT
20063975 TATAAATATCTCAAATATTAT
1 TATAAATATCTCAAATATTAT
20063996 TATAAAT
1 TATAAAT
20064003 GTATAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.28
20 1 0.04
21 17 0.68
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (21 bp):
TATAAATATCTCAAATATTAT
Found at i:20066037 original size:3 final size:3
Alignment explanation
Indices: 20066029--20066061 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20066019 CATTGAAAAT
20066029 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20066062 GTTGCTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20071020 original size:25 final size:25
Alignment explanation
Indices: 20070992--20071048 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
20070982 CGGTAAACAG
*
20070992 TAAGCTCCTCCAAGTTGAATAACGA
1 TAAGCTCCTCCAAGCTGAATAACGA
* * * *
20071017 TAAGATCCTCCGAGCTGAATAATGG
1 TAAGCTCCTCCAAGCTGAATAACGA
20071042 TAAGCTC
1 TAAGCTC
20071049 ATACGAGCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (25 bp):
TAAGCTCCTCCAAGCTGAATAACGA
Found at i:20071055 original size:25 final size:25
Alignment explanation
Indices: 20071027--20071082 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
20071017 TAAGATCCTC
*
20071027 CGAGCTGAATAAT-GGTAAGCTCATA
1 CGAGCTGAAT-ATCAGTAAGCTCATA
*
20071052 CGAGCTGAGTATCAGTAAGCTCATA
1 CGAGCTGAATATCAGTAAGCTCATA
*
20071077 AGAGCT
1 CGAGCT
20071083 AAAATTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (25 bp):
CGAGCTGAATATCAGTAAGCTCATA
Found at i:20074143 original size:50 final size:50
Alignment explanation
Indices: 20074048--20074144 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
20074038 CATTGAGATT
* * * *
20074048 ATGAGAGGTCCCATGTAAGACCTTGTCTGGGACATGGCGTTGGTACCTAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGTACCTAG
* *
20074098 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGTATGGGTACC
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGTACC
20074145 GATGTGGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.24
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGTACCTAG
Found at i:20074457 original size:12 final size:12
Alignment explanation
Indices: 20074440--20074478 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
20074430 ATGAGTTTTT
20074440 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
20074452 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
20074464 TAAGTGAGTAAG
1 TAAGTAAGCAAG
20074476 TAA
1 TAA
20074479 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:20078325 original size:21 final size:23
Alignment explanation
Indices: 20078288--20078352 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
20078278 CCTGATCAAT
* *
20078288 ATACGACACA-TAAGTGCCTG-G
1 ATACGACACACAAAGTGCCTGAA
20078309 A-ACGACACACAAAGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
* *
20078331 ATACGACACATAAAGTACCTGA
1 ATACGACACACAAAGTGCCTGA
20078353 TCGACAAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.22
21 10 0.27
22 1 0.03
23 18 0.49
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:20079554 original size:21 final size:21
Alignment explanation
Indices: 20079530--20079572 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
20079520 AATTGCTCTC
20079530 TGTTTCTTT-TCTTCTTTGTTT
1 TGTTTCTTTGT-TTCTTTGTTT
20079551 TGTTTCTTTGTTTCTTTGTTT
1 TGTTTCTTTGTTTCTTTGTTT
20079572 T
1 T
20079573 TTTACTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.77
Consensus pattern (21 bp):
TGTTTCTTTGTTTCTTTGTTT
Found at i:20085120 original size:21 final size:20
Alignment explanation
Indices: 20085076--20085120 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
20085066 GAAATTTTTT
* *
20085076 TAAATATTATTAATTAATTA
1 TAAATATTATTAATCAACTA
*
20085096 TAAATTTTATTAAATCAACTA
1 TAAATATTATT-AATCAACTA
20085117 TAAA
1 TAAA
20085121 ACTCAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATATTATTAATCAACTA
Found at i:20086930 original size:16 final size:16
Alignment explanation
Indices: 20086911--20086968 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
20086901 TAAAATACTT
20086911 TAAATTGTATTAGAGG
1 TAAATTGTATTAGAGG
* *
20086927 TAAATTTTTAATTTTAAAGG
1 TAAA-TTGT-A--TTAGAGG
20086947 TAAATTGTATTAGAGG
1 TAAATTGTATTAGAGG
*
20086963 TGAATT
1 TAAATT
20086969 TTTAAAATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 15 0.45
17 3 0.09
18 2 0.06
19 3 0.09
20 10 0.30
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (16 bp):
TAAATTGTATTAGAGG
Found at i:20086994 original size:22 final size:22
Alignment explanation
Indices: 20086969--20087012 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20086959 GAGGTGAATT
20086969 TTTAAAATACTTTA-ATTACATC
1 TTTAAAAT-CTTTATATTACATC
*
20086991 TTTAAAATTTTTATATTACATC
1 TTTAAAATCTTTATATTACATC
20087013 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAAAATCTTTATATTACATC
Found at i:20087018 original size:22 final size:21
Alignment explanation
Indices: 20086979--20087019 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
20086969 TTTAAAATAC
**
20086979 TTTAATTACATCTTTAAAATT
1 TTTAATTACATCAATAAAATT
20087000 TTTATATTACATCAATAAAA
1 TTTA-ATTACATCAATAAAA
20087020 AATTTTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAATTACATCAATAAAATT
Found at i:20087424 original size:27 final size:27
Alignment explanation
Indices: 20087372--20087442 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
20087362 AAAAATAAAA
* *
20087372 ATTTACTAAAATACTATAAGTTTTTTTT
1 ATTTACCAAAATA-TATAAATTTTTTTT
20087400 ATTTACCAAAATATATAAATTTTTTTT
1 ATTTACCAAAATATATAAATTTTTTTT
20087427 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
20087443 CAAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 29 0.71
28 12 0.29
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATATAAATTTTTTTT
Found at i:20087652 original size:11 final size:11
Alignment explanation
Indices: 20087636--20087672 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
20087626 GTTGGCGCGG
20087636 AAAAGAAGAGA
1 AAAAGAAGAGA
20087647 AAAAG-AGAGA
1 AAAAGAAGAGA
*
20087657 AAAAGAGGAGA
1 AAAAGAAGAGA
20087668 AAAAG
1 AAAAG
20087673 GAGGTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:20087737 original size:19 final size:21
Alignment explanation
Indices: 20087699--20087737 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
20087689 AATAATTGAT
*
20087699 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
20087720 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
20087738 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:20087816 original size:3 final size:3
Alignment explanation
Indices: 20087810--20087847 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20087800 ATTATTATTA
20087810 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
20087848 AGTATTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:20088109 original size:12 final size:12
Alignment explanation
Indices: 20088092--20088122 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20088082 ATAATTTTAG
20088092 TGTGTATTATTT
1 TGTGTATTATTT
20088104 TGTGTATTATTT
1 TGTGTATTATTT
*
20088116 TGAGTAT
1 TGTGTAT
20088123 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:20093777 original size:21 final size:22
Alignment explanation
Indices: 20093751--20093802 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
20093741 TTGTGCCGCC
*
20093751 TTTTTTTCCCCTCCATCA-CCT
1 TTTTTTTCCCCTACATCACCCT
20093772 TTTTTTTCCCCTACATCACCCT
1 TTTTTTTCCCCTACATCACCCT
20093794 TTTTTTTCC
1 TTTTTTTCC
20093803 TATATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.10, C:0.38, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTTTTCCCCTACATCACCCT
Found at i:20094580 original size:4 final size:4
Alignment explanation
Indices: 20094564--20094713 Score: 105
Period size: 4 Copynumber: 37.0 Consensus size: 4
20094554 CTCCTTTCCT
* *
20094564 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTC CTTC TCTTC -TTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTTC TTTC T-TTC TTTC
* * *
20094613 -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCCC TTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT--C TTTC TTTC TTTC TTTC
* * * *
20094660 TTTC TTTC TTCCC TCTC ATTTC TTCC TTTC TTTC TCTC TTTC TTTC TTTC
1 TTTC TTTC TT-TC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
20094710 TTTC
1 TTTC
20094714 CCTCCCCTTC
Statistics
Matches: 116, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
3 15 0.13
4 80 0.69
5 15 0.13
6 6 0.05
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:20094594 original size:52 final size:48
Alignment explanation
Indices: 20094536--20094632 Score: 121
Period size: 48 Copynumber: 2.1 Consensus size: 48
20094526 TTCCCTCTTC
* *
20094536 TTCTTCTTTTTTTCTCTTCTCCTT-TC--CTT-TTCTTTCCTTCTTTCT
1 TTCTT-TTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCCTTCTTTCT
* *
20094581 TTCTTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTTTCTTTTT
1 TTCTTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCCTTCTTTCT
20094629 TTCT
1 TTCT
20094633 CTTCTCCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
44 16 0.36
45 7 0.16
47 3 0.07
48 18 0.41
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (48 bp):
TTCTTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCCTTCTTTCT
Found at i:20094597 original size:44 final size:43
Alignment explanation
Indices: 20094536--20094712 Score: 163
Period size: 44 Copynumber: 4.1 Consensus size: 43
20094526 TTCCCTCTTC
*
20094536 TTCTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCT
1 TTCTT-TTTTCTTCTCTTCTCCTTT-CTTTTCTTTCCTTCTTTCT
* *
20094581 TTCTTTTTTCTTCTCTTTTCC-TTCTCTTC-TT-CTTCTTTCT
1 TTCTTTTTTCTTCTCTTCTCCTTTCTTTTCTTTCCTTCTTTCT
*
20094621 TTC-TTTTT-TTCTCTTCTCCTTTCCCTTTCTTTCCTTC-TT-T
1 TTCTTTTTTCTTCTCTTCTCCTTT-CTTTTCTTTCCTTCTTTCT
* * * *
20094661 TTCTTTCTTCCCTCTCATTTCTTCCTTTC-TTTCTCTCTTTCTTTCT
1 TTCTTT-TTTCTTCTC--TTC-TCCTTTCTTTTCTTTCCTTCTTTCT
20094707 TTCTTT
1 TTCTTT
20094713 CCCTCCCCTT
Statistics
Matches: 110, Mismatches: 10, Indels: 23
0.77 0.07 0.16
Matches are distributed among these distances:
38 10 0.09
39 7 0.06
40 20 0.18
41 8 0.07
42 11 0.10
43 6 0.05
44 24 0.22
45 11 0.10
46 13 0.12
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.68
Consensus pattern (43 bp):
TTCTTTTTTCTTCTCTTCTCCTTTCTTTTCTTTCCTTCTTTCT
Found at i:20094643 original size:82 final size:79
Alignment explanation
Indices: 20094504--20094713 Score: 255
Period size: 82 Copynumber: 2.6 Consensus size: 79
20094494 AAATTACCTT
* * * *
20094504 TTTTTTCTTTTTTTTTCCTTCCTTCCCTCTTC-TTC-TTCTTTTTTTCTCTTCTCCTTTCCTTTT
1 TTTTTTCTTCTCTTTTCCTTCCTT-CTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTT
20094567 CTTTCCTTCTTTCTTTC
65 CTTTCCTTC-TT-TTTC
20094584 TTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTT
1 TTTTTTCTTCTCTTTTCCTTC-CTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTT
20094649 CTTTCCTTCTTTTTC
65 CTTTCCTTCTTTTTC
* * * *
20094664 TTTCTTCCCTCTCATTT-CTTCCTTTCTTTCTCTCTTTCTTTCTTTCTTTC
1 TTT-TTTCTTCTCTTTTCCTTCC-TTC-TTCT-TCTTTCTTTCTTTTTTTC
20094714 CCTCCCCTTC
Statistics
Matches: 115, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
79 1 0.01
80 39 0.34
81 22 0.19
82 53 0.46
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (79 bp):
TTTTTTCTTCTCTTTTCCTTCCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTC
TTTCCTTCTTTTTC
Found at i:20094651 original size:74 final size:70
Alignment explanation
Indices: 20094530--20094716 Score: 179
Period size: 70 Copynumber: 2.6 Consensus size: 70
20094520 CCTTCCTTCC
* *
20094530 CTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTC-CTT-TTCTTT-CC-TTCTTTCTTTCTTTTTTC
1 CTCTTCTTCTTCTTTCTTTCT-TT-T--TTTCTCTTCTTCTTTCCCTTTCTTTCCTTC-TTTTTC
*
20094591 TTCTCTTTTCCTT
61 TT-TC--TTCCCT
*
20094604 CTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTTTCTTTCT
1 CTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTTCTTTCCCTTTCTTTCCTTCTTTTTCTTTCT
20094669 TCCCT
66 TCCCT
* * *
20094674 CTCAT-TTCTTCCTTTCTTTCTCTCTTTCT-TTCTTTCTTTCCCT
1 CTCTTCTTCTT-CTTTCTTTCTTTTTTTCTCTTC-TTCTTTCCCT
20094717 CCCCTTCTGC
Statistics
Matches: 99, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
69 8 0.08
70 38 0.38
71 3 0.03
72 8 0.08
73 12 0.12
74 30 0.30
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (70 bp):
CTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTTCTTTCCCTTTCTTTCCTTCTTTTTCTTTCT
TCCCT
Found at i:20094896 original size:26 final size:26
Alignment explanation
Indices: 20094838--20094906 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 26
20094828 AGTTTTTTTG
20094838 ATATATTTTGGTAAATAAAAAAAAATT
1 ATATATTTTGGTAAAT-AAAAAAAATT
*
20094865 ATATATTTTGGTAAAT-AAAAAAGTT
1 ATATATTTTGGTAAATAAAAAAAATT
20094890 ATAATATTTTGGTAAAT
1 AT-ATATTTTGGTAAAT
20094907 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
25 10 0.25
26 14 0.35
27 16 0.40
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (26 bp):
ATATATTTTGGTAAATAAAAAAAATT
Found at i:20099471 original size:41 final size:40
Alignment explanation
Indices: 20099398--20099535 Score: 152
Period size: 41 Copynumber: 3.3 Consensus size: 40
20099388 TTTCAGAAAA
*
20099398 CGCCGCTAATGCTCTACCTTTTTAGCGGCGTTTTTGAAGAAG
1 CGCCGCTAATGCTCTACC--TTTAGCGACGTTTTTGAAGAAG
**
20099440 CGTTGCTAATGCTCTATCCTTTAGCGACGTTTTTGAAGAAG
1 CGCCGCTAATGCTCTA-CCTTTAGCGACGTTTTTGAAGAAG
* * * *
20099481 CGCCGGTAATGCTCTGGCCTTTAGCGGGA-TTTTTTGAATAAG
1 CGCCGCTAATGCTCT-ACCTTTAGC--GACGTTTTTGAAGAAG
20099523 CGCCGCTAATGCT
1 CGCCGCTAATGCT
20099536 AAGATCTTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
41 41 0.50
42 37 0.45
43 4 0.05
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (40 bp):
CGCCGCTAATGCTCTACCTTTAGCGACGTTTTTGAAGAAG
Found at i:20099545 original size:42 final size:42
Alignment explanation
Indices: 20099469--20099549 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
20099459 TTTAGCGACG
* ** *
20099469 TTTTTGAAGAAGCGCCGGTAATGCTCTGGCCTTTAGCGGGAT
1 TTTTTGAAGAAGCGCCGCTAATGCTAAGACCTTTAGCGGGAT
* *
20099511 TTTTTGAATAAGCGCCGCTAATGCTAAGATCTTTAGCGG
1 TTTTTGAAGAAGCGCCGCTAATGCTAAGACCTTTAGCGG
20099550 CGCTTTTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (42 bp):
TTTTTGAAGAAGCGCCGCTAATGCTAAGACCTTTAGCGGGAT
Found at i:20099557 original size:42 final size:40
Alignment explanation
Indices: 20099418--20099557 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 40
20099408 GCTCTACCTT
** **
20099418 TTTAGCGGCGTTTTTGAAGAAGCGTTGCTAATGCTCTATCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTAGAT-C
* * * **
20099459 TTTAGCGACGTTTTTGAAGAAGCGCCGGTAATGCTCTGGCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCT-AGATC
*
20099500 TTTAGCGG-GATTTTTTGAATAAGCGCCGCTAATGCTAAGATC
1 TTTAGCGGCG--TTTTTGAAGAAGCGCCGCTAATGCT-AGATC
20099542 TTTAGCGGCGCTTTTT
1 TTTAGCGGCG-TTTTT
20099558 CATATTTTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
40 1 0.01
41 39 0.49
42 38 0.48
43 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTAGATC
Found at i:20099868 original size:15 final size:16
Alignment explanation
Indices: 20099848--20099881 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
20099838 CAAATATGGT
*
20099848 GTTTATGGATTT-AGG
1 GTTTATAGATTTAAGG
20099863 GTTTATAGATTTAAGG
1 GTTTATAGATTTAAGG
20099879 GTT
1 GTT
20099882 AGAGGTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (16 bp):
GTTTATAGATTTAAGG
Found at i:20100018 original size:21 final size:21
Alignment explanation
Indices: 20099966--20100038 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
20099956 TCTGGGTTGG
*
20099966 GGTTTAGGGATTAGGGATTTAA
1 GGTTTAGGGGTTA-GGATTTAA
*
20099988 GG--T-CGGGTTAGGATTTAA
1 GGTTTAGGGGTTAGGATTTAA
**
20100006 GGTTTAGGGGTTAGG-GCTAGA
1 GGTTTAGGGGTTAGGATTTA-A
20100027 GGTTTAGGGGTT
1 GGTTTAGGGGTT
20100039 TAGGGGTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 10 0.24
19 5 0.12
20 4 0.10
21 21 0.50
22 2 0.05
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.34
Consensus pattern (21 bp):
GGTTTAGGGGTTAGGATTTAA
Found at i:20100068 original size:29 final size:28
Alignment explanation
Indices: 20099997--20100072 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
20099987 AGGTCGGGTT
*
20099997 AGGATTTAAGGTTTAGGGGTTAGGGCTAG
1 AGGATTTAA-GTTTAGGGGTTAGAGCTAG
*
20100026 AGG-TTTAGGGGTTTAGGGGTTAAGAGCTA-
1 AGGATTTA--AGTTTAGGGGTT-AGAGCTAG
20100055 AGGATTTATAGTTTAGGG
1 AGGATTTA-AGTTTAGGG
20100073 TTTCATGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 4 0.10
29 25 0.64
30 10 0.26
ACGTcount: A:0.25, C:0.03, G:0.39, T:0.33
Consensus pattern (28 bp):
AGGATTTAAGTTTAGGGGTTAGAGCTAG
Found at i:20100381 original size:23 final size:23
Alignment explanation
Indices: 20100337--20100382 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20100327 TATGGTTTAA
* * *
20100337 GGTTTAGGGGTTAGGAGTTAGGG
1 GGTTTAAGGGTTAAGAGCTAGGG
*
20100360 GGTTTAAGGGTTAATAGCTAGGG
1 GGTTTAAGGGTTAAGAGCTAGGG
20100383 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.02, G:0.46, T:0.30
Consensus pattern (23 bp):
GGTTTAAGGGTTAAGAGCTAGGG
Found at i:20101133 original size:22 final size:23
Alignment explanation
Indices: 20101094--20101137 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
20101084 CAAATGTGGA
20101094 AGAAAATAAAAGATAATTAAAAT
1 AGAAAATAAAAGATAATTAAAAT
20101117 AGAAAA-AAAATGA-AATTAAAA
1 AGAAAATAAAA-GATAATTAAAA
20101138 CACTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (23 bp):
AGAAAATAAAAGATAATTAAAAT
Found at i:20103454 original size:12 final size:12
Alignment explanation
Indices: 20103439--20103472 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20103429 TAACCTACAT
20103439 AACTTACATAGA
1 AACTTACATAGA
*
20103451 AACTTATATAGA
1 AACTTACATAGA
*
20103463 AACTTGCATA
1 AACTTACATA
20103473 ACTTACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (12 bp):
AACTTACATAGA
Found at i:20103531 original size:16 final size:16
Alignment explanation
Indices: 20103512--20103622 Score: 65
Period size: 16 Copynumber: 7.2 Consensus size: 16
20103502 ATACATAGCG
20103512 TACATAACTTACATAA
1 TACATAACTTACATAA
**
20103528 TACACCACTTACAT-A
1 TACATAACTTACATAA
*
20103543 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
**
20103557 TACACCACTT-CAT-A
1 TACATAACTTACATAA
*
20103571 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
* * *
20103585 TACATAGCCTACGTAA
1 TACATAACTTACATAA
*
20103601 CTTACTTAACTTACATAA
1 --TACATAACTTACATAA
20103619 TACA
1 TACA
20103623 CCACTTACGT
Statistics
Matches: 68, Mismatches: 18, Indels: 18
0.65 0.17 0.17
Matches are distributed among these distances:
12 5 0.07
13 12 0.18
14 4 0.06
15 6 0.09
16 29 0.43
18 12 0.18
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (16 bp):
TACATAACTTACATAA
Done.